Open a ptraj.in and add the following lines:
trajin rec.all.mdcrd
strip :WAT,Na+,Cl-
trajout rec.mdnw.mdcrd
Now enter ptraj rec.top < ptraj.in
But if you need some waters around your ligand or QMMM region? No problem! Forget 'strip' and add these lines to your ptraj.in:
solvent byres :WAT
closestwater 20 :464 first (WAT around residue 464 until 20 A of distance will be preserved)